Fabrication and packaging of suspended microchannel detectors

ABSTRACT

An apparatus for detecting an analyte in solution that has a suspended beam containing at least one microfluidic channel containing a capture ligand that bonds to or reacts with an analyte. The apparatus also includes at least one detector for measuring a change in the beam upon binding or reaction of the analyte. A method of making the suspended microfluidic channels is disclosed, as well as, a method of integrating the microfluidic device with conventional microfluidics having larger sample fluid channels.

GOVERNMENT SUPPORT

The work described herein was supported, in part, by grants from theDefense Advanced Research Projects Agency (DARPA) (MDA972-001-1-003).The United States government may have certain rights in the invention.

BACKGROUND

Conventional procedures based on two-dimensional gel electrophoresis forprofiling the concentrations of specific proteins and their byproductsare time-consuming, labor-intensive, and require significant technicalexpertise to obtain quantitative information. One approach forcircumventing these limitations is to develop the equivalent of a DNAmicroarray for proteins. Protein microarrays consist of various types ofcapture ligands that exhibit a high binding affinity toward a particularprotein. Target proteins are either labeled with a fluorescent label, oradditional fluorescently labeled protein is used to selectively bind tothe target once it has been capture to a specific site on the array. Thelatter approach, often referred to as a sandwich assay, has theadvantage of being extremely selective since very rarely will a targetprotein bind to both the capture molecule and an additional protein.This disadvantage of the sandwich assay is that there are a limitednumber of target proteins for which there exist two distinct bindingpartners. As a result, direct labeling of the target protein can be mostgenerally applied for profiling multiple proteins from a cell lysate.However, there are two drawbacks of direct labeling: First, theefficiency of coupling fluorescent labels to low abundance proteinswithin a lysate is highly variable. This can often make it difficult toachieve sufficient sensitivity as well as reliability. Second, thecomplexity of protein structures poses significant challenges forattaching labels to specific sites while preserving the functionality ofa protein. This challenge was cogently summarized by biophysicist S. P.Fordor: “Conventional detection techniques based on fluorescent taggingrequire that one partner of a complex is chemically modified. Thesemodifications can subtly alter molecular interactions by changing thechemical nature of the binding interaction.” Mazzoila, L. T. and Fordor,S. P. A., Biophys. J. (1995), 68: 1653-1660, the entire teachings ofwhich are incorporated herein by reference. Thus, eliminating thelabeling process will improve the feasibility, speed, and utility ofquantitative protein assays.

The major limitation of existing label-free detectors is that they aresignificantly less sensitive than fluorescence detection. The two mostwell known approaches are the quartz crystal microbalance (QCM) fordetecting surface adsorbed mass and the surface plasmon resonance (SPR)technique for detecting refractive index changes in close proximity to ametal surface. Both methods have significant fundamental limitationsconcerning scalability, sensitivity to low-concentration samples, andtheir ability to provide quantitative information. The mass resolutionof the QCM is on the order of 10⁻¹⁷ g/μm², which corresponds to about100 proteins/μm² (assuming a molecular weight 100 kDa). Furthermore, theQCM sensor area is macroscopic in scale (typically a few mm²), so theminimum detectable mass is on the order of several nanograms, or 10¹⁰molecules. This detection level is not suitable for many biologicalassays. Fluorescence routinely resolves 1-10 molecules for a surfacearea less than 100 μm². The QCM also requires that the capture ligandsbe rigidly coupled to the sensor surface. This limits the efficiency ofthree-dimensional coatings (e.g. carboxymethyldextran (CMD) matrix) thatenhance the effectiveness of mass sensing.

The SPR, which achieves a similar resolution as the QCM, measureschanges in the refractive index that occur within a CMD layer above thesensor surface several hundred nanometers thick. Since the influence ofthe target molecules on the optical properties of this layer isgenerally unknown, SPR usually provides indirect information. This canmake it difficult to quantify the amount of bound target molecules.Furthermore, attempts to reduce the sensor surface area for large-scaleintegration are not yet capable of reaching sensitivity levels that arecomparable to commercial macroscopic instruments. This limitation isoften attributed to the difficulty of matching the very narrow operatingrange of the integrated optics to the refractive index of typical buffersolutions using materials available for microfabrication.

The development of label-free detectors that are both sensitive andscalable (both down in sensor area and up in number of sensors) is inits infancy. In addition to on-going research for advancing opticalmethods as well as acoustical methods such as the flexural plate wavedevice (FPW), there are several new approaches for label-free detectionthat are currently being pursued. One approach for molecular detectionis the transduction of surface binding events on a microcantilever intomechanical bending. The bending is not induced by the addition of massbut rather the change in surface energy resulting from specific bindingof the biomolecules. For example, it has been shown that amicrocantilever stress sensor can detect DNA hybridization. In otherwork, it has been shown that the microcantilever stress sensor candetect prostate-specific antigen (PSA) in a background of human serumalbumin and human plasminogen (Wu et al., Nature Biotech. (2001), 19:856, the entire teachings of which are incorporated herein byreference). This result suggests that the stress sensor could be aclinically relevant diagnostic technique for prostate cancer.

The advantage of using microcantilevers for label-free detection is thatthis technique is scalable. For example, researchers at IBM Zurich havedemonstrated that eight cantilevers can be detected in parallel (Arntz,et al., Nanotechnology (2003), 14(1): 86 and Battiston, et al., Sensorsand Actuators B-Chemical (2001), 77(1 and 2): 122-131, the entireteachings of which are incorporated herein by reference). However, thereare three drawbacks to using the microcantilever stress sensor. First,there is not yet a viable approach for integrating the cantilevers withconventional microfluidics. Currently, the surfaces must befunctionalized by manually aligning micropipettes to each cantileverbefore packaging the cantilevers within a macroscopic fluid cell.Second, the surface stress induced by molecular binding must occur ononly one side of the cantilever in order for it to bend. This requiresdifferent surface chemistries to be developed for the top and bottomsides of the sensor. Third, it has not yet been demonstrated (orpredicted) that the stress sensor has a higher resolution (in terms ofminimum number of detectable molecules per area) than commerciallyavailable sensors such as the SPR. Despite these limitations, thedevelopment of the microcantilever stress sensor is still in its infancyand its full potential has yet to be realized.

Finally, resonant cantilever mass sensors, while successful for chemicalsensing in gaseous environments, have received less attention forbiomolecular detection in solution. This is primarily because the masssensitivity and frequency resolution are significantly degraded by thelow quality factor and large effective mass that is induced by viscousdrag. While the quality factor can be enhanced by using electronicfeedback known as Q-control, the mass sensitivity, in terms of frequencyshift per mass loading, is not improved.

Accordingly, there remains a need for an analytical technique that issufficiently sensitive but does not require modification of the analyteof interest.

SUMMARY OF THE INVENTION

The present invention relates to an apparatus that is a label-freedetector for measuring a property of an analyte. The apparatus comprisesat least one suspended beam connected to two mechanically stablesupports. The suspended beam may contain one or more microfluidicchannels, and each microfluidic channel has at least one chemicalspecies that binds to or reacts with the analyte. The apparatus alsocomprises one or more detectors for measuring a change in the one ormore beams upon binding or reaction of the analyte. In one embodiment,the suspended beam is resonating.

One disadvantage of a cantilever microfluidic channel is that the samplefluid must enter and exit the microfluidic channel through the end ofthe cantilever that is attached to the semiconductor wafer. Thus, acantilever having a microfluidic channel must have a sharp bend at thefree end of the cantilever where the channel doubles back on itself toexit through the attached end of the cantilever. A detector having asuspended beam connected to two mechanically stable supports with amicrofluidic channel that flows through the beam is often preferable toa cantilever type beam because the microfluidic channel contains nosharp bends and thus components of the sample fluid other than theanalyte are less likely to collect in the microcrofluidic channel.

In another embodiment, the apparatus of the invention for detecting ananalyte or measuring a property of the analyte, comprises a devicestructure that has at least one suspended beam that contains one or moremicrofluidic channels, wherein each microfluidic channel has at leastone chemical species that binds to or reacts with an analyte; and asample fluid channel having a depth that is substantially larger thanthe microfluidic channel connected to the inlet of at least one of themicrofluidic channel. The apparatus may also include one or moredetectors for measuring a change in the beam upon binding or reacting ofthe analyte. In this embodiment, the suspended beam may be either acantilever or the beam may be suspended between two mechanically stablesupports. In one preferred embodiment, the apparatus is amicro-electro-mechanical system (MEMS) that has a packaging structurethat covers the device region. In one embodiment, the packagingstructure is sealed to the device region such that the suspended beam isin a controlled environment. This allows the device to be protected fromenvironmental factors, such as variations in humidity, dust particles,static charge build-up, ect., that could decrease the signal to noiseratio of the device. In one embodiment the packaging structure is sealedto the device region such that the suspended beam is in a low pressureenvironment (i.e., an environment that is less than atmosphericpressure).

In another aspect, the invention is related to a method of fabricating afunctionalized microfluidic channel having an inlet and an outlet. Themethod involves depositing a first channel layer on a semiconductorwafer having one or more trenches. A sacrificial layer is deposited onthe first insulator layer, then a planarization technique, such aschemical-mechanical polishing, is used to remove the sacrificial layerdown to the first channel layer, thereby exposing a planar surface ofthe first insulator layer having the sacrificial layer in the trenches.A second channel layer is deposited on the planar surface, and one ormore holes are formed in the second channel layer that are connected toone or more of the trenches. The sacrificial layer, or a portionthereof, is then removed from the trenches by etching, thereby forming amicrofluidic channel. The interior of the microfluidic channels is thenfunctionalized with a capture ligand. The functionalization step maytake place either before or after a packaging structure containingconnections with sample fluid channels is added to the device containingthe microfluidic channels. In one embodiment, a portion of the backsideof the semiconductor wafer (i.e., the side of the semiconductor waferopposite to the side on which the channel layers are deposited) isremoved below the microfluidic channel thereby forming a suspendedmicrochannel. Preferably, the portion of the semiconductor wafer belowthe microfluidic channel is etched back to the first channel layer. Inone embodiment, the backside of the semiconductor wafer is etchedsimultaneously with removal of the sacrificial layer from the trenches.In one preferred embodiment, the semiconductor wafer is a silicon wafer,the first and the second channel layers are silicon nitride or silicondioxide and the sacrificial layer is polysilicon. In this embodiment, aportion of the sacrificial layer may be doped with either a p-type orn-type dopant. Heavily doped polysilicon (e.g., a dopant concentrationof about 5×10¹⁹ cm⁻³ or greater) is resistant to etching with potassiumhydroxide. Thus, the sacrificial layer may be removed by etching with apotassium hydroxide and the heavily doped areas will remain in themicrofluidic channel. The heavily doped polysilicon areas of the channelwill be electrically conductive. Alternatively, the microfluidic channelmay be made electrically conductive by having the first and the secondchannel layers that are made from heavily doped polysilicon.

Using the method of the invention, very thin microfluidic channelshaving very thin walls may be formed with the method of the invention.The sensitivity of a resonant mass detector is enhance by decreasing thethickness of the resonating beam. In addition, the method may be used toform microfluidic channels from materials that are not amenable to waferbonding, such as silicon nitride.

In another aspect, the invention is related to a packaged a devicecomprising one or more suspended microfluidic channel formed in asemiconductor wafer, and a method of making the same. The methodinvolves patterning a substrate with one or more separately addressableelectrodes, wherein the electrodes can be aligned with each microfluidicchannel of the device; preparing a poly(dimethyl siloxane) gasket havingone or more fluid channels and one or more opening; bonding the gasketto the substrate; patterning a common electrode on the surface of thedevice, wherein the common electrode is formed on each microfluidicchannel; and bonding the gasket to the device, wherein the fluidchannels of the gasket connect with the inlets and outlets of themicrofluidic channels of the device and each opening on the gasket isaligned with one or more suspended microfluidic channel.

In another embodiment, the invention involves a method of packaging adevice comprising one or more suspended microfluidic channels formed ina semiconductor wafer. The method involves forming one or more fluidchannel and one or more cavities in a substrate, wherein the cavitiescan be aligned with the microfluidic channels; patterning the cavitiesof the substrate with one or more separately addressable electrodes,thereby forming electrodes that can be aligned with each microfluidicchannel of the device; patterning a common electrode on the surface ofthe device, wherein the common electrode is formed on each microfluidicchannel; and bonding the substrate to the device, wherein the fluidchannels of the substrate connect with the inlets and outlets of themicrofluidic channels of the device and each trench of the substrate isaligned with one or more suspended microfluidic channel.

In another embodiment, the invention relates to a method of packaging adevice comprising one or more suspended microfluidic channel formed in asemiconductor wafer. The method involves patterning a surface of asubstrate with one or more separately addressable electrodes; forming aphotoresist on the surface of the patterned substrate; irradiating thephotoresist through a mask, thereby removing the photoresist frompredetermined areas of the substrate; electroplating a metal in the areaof the substrate where the photoresist was removed, thereby forming thewalls of the one or more microfluidic channels and the walls of the oneor more cavities; removing the remainder of the photoresist; patterninga common electrode on a surface of the device having an inlet and anoutlet for each of the microfluidic channels; and bonding theelectroplated metal to the common electrode, wherein the fluid channelsformed by the electroplated metal walls connect with the inlets andoutlets of the microfluidic channels of the device and each cavityformed by the electroplated metal walls is aligned with one or moresuspended microfluidic channel.

The packaging methods of the invention allow for the microfluidicchannels to be in a controlled environment and allow the microfluidicchannels of the device to be connected to larger sample fluid channels.In addition, the packaging methods integrate drive electrodes anddetectors that provide the electrostatic driving force that causes eachmicrofluidic channel to resonate. Thus, the packaging methods of theinvention allow hundreds of devices to be produced from a single wafer.

BRIEF DESCRIPTION OF THE DRAWING

The invention is described with reference to a particular embodimentshown in the figures. The embodiment in the figures is shown by way ofexample and is not meant to be limiting in any way.

FIG. 1 is a schematic representation of one embodiment of an apparatusof the invention that has a suspended beam connected to two mechanicallystable supports.

FIG. 2 is a schematic representation of one embodiment of an apparatusof the invention that has a cantilever suspended beam.

FIG. 3 is a schematic representation of a suspended beam having twomicrofluidic channels that converge within the beam at a point that isplugged by a gel then diverge.

FIG. 4 is a schematic representation of one embodiment of an apparatusof the invention that is packaged using a polydimethyl siloxane gasket.

FIG. 5 is a schematic representation of one embodiment of an apparatusof the invention that has a substrate joined directly to the device byanodic bonding.

FIGS. 6A-6E are a schematic representation of a manufacturing process ofone embodiment of an apparatus of the invention that has a packagingstructure with a flip-chip configuration. FIG. 6F is a schematicrepresentation of the packaged apparatus.

FIG. 7 shows multiple devices fabricated on one silicon wafer.

FIGS. 8A-8H are a schematic representation of one embodiment of themethod of the invention for fabricating microfluidic channels.

FIG. 9A is an electron micrograph of three suspended microfluidicchannels.

FIG. 9B is a phase contrast optical image of three suspendedmicrofluidic channels.

FIG. 10 are normalized frequency response curves of a 300 μm longcantilever filled with air, 2-propanol and water.

FIG. 11A-D are the relative frequency shift for a 40 kHz resonantmicrofluidic channel after injection of (A) buffer, (B) avidin, (C)bBSA, and (D) avidin.

DETAILED DESCRIPTION

The apparatus of the invention is a new method of detecting biomoleculeswhereby a suspended microfluidic channel is used to capture specifictarget molecules onto the interior channel walls. The amount of boundtarget molecules is determined by measuring the change in resonantfrequency during the adsorption. There are three key properties thatenable this method of detection: First, the mass density of biomoleculesis different than the density of the water. For example, proteins have amass density in the range of 1.3-1.4 g/cm³. Thus, the net mass of thefluid-filled resonator depends on the total number of biomolecules thatare contained within the resonator. Second, the difference in energyloss of the resonator (quality factor, Q) between an air-filled andfluid-filled microchannel is insignificant. As a result, the masssensitivity as well as the frequency detection resolution are notdegraded by viscous drag of the solution. This is not the case forresonating detectors where the capture ligands are on the externalportion of beam that is immersed in a solution containing the analyte.Resonating detectors of this type have a low quality factor due toviscous drag of the solution. Third, the surface to volume ratio of themicrochannel must be sufficiently large such that number ofsurface-bound molecules is generally much large than the number ofmolecules contained within the microchannel volume. Thus, the binding oftarget biomolecules to the microchannel walls can be monitored inreal-time.

The suspended microfluidic channel detector enables the extraordinaryhigh mass resolution associated with a resonator in vacuum whilepreserving the highly selective biomolecular recognition that occursonly within the aqueous environment. In other words, the targetmolecules (or analytes) that bind to the capture ligands within theoscillating microchannel are not aware that the exterior of the channelis vacuum, or a gas. Suspended microfluidic channels are also scalableand allow analytes to be detected in a low volume of sample fluid (˜10pL per detector)

Decreasing the channel thickness and the thickness of the walls of thechannel, as well as, increasing the number of capture ligands bound tothe interior of the channel should increase the resolution. Integratingmicrofluidic channel detectors with conventional microfluidics willincrease the utility of such detectors and allow multiple detectors tobe fabricated on one semiconductor wafer. It has been predicted that asuspended microchannel with a surface area of 10⁴ μm² should be capableof resolving ˜1 protein/μm² (assuming a 100 kD protein mass).

A resonant mass sensor with internal surface area A can be modeled as aharmonic oscillator with an effective mass m and resonance frequency f.The relative frequency shift Δf/f resulting from a small surface massloading Δσ=Δm/A is given to first order by equation (1): $\begin{matrix}{\frac{\Delta\quad f}{f} = {{- \frac{1}{2}}{\left( \frac{A}{m} \right) \cdot {\Delta\sigma}}}} & (1)\end{matrix}$

Equation (1) shows that for a given detectable frequency shift Δf and aresonance frequency f, the smallest detectable surface mass loading isfully determined by the ratio of surface area to total mass. This ratiocan be improved by reducing the thickness of the fluid layer as well asthat of the channel walls.

In one embodiment, the apparatus 10 (see FIG. 1) of the invention fordetecting an analyte or measuring a property of an analyte, comprises atleast one suspended beam 12 connected to two mechanically stablesupports 14 a and 14 b, wherein the beam contains one or moremicrofluidic channels 16; and one or more detectors (not shown). In analternative embodiment, the beam may be a cantilever (see FIG. 2). Amicrofluidic channel is a channel that has an inlet and an outlet and adepth and a height in the range of between about 50 nm and about 2000nm. In one embodiment, the microfluidic channel has a depth in the rangeof between about 100 nm and about 1200 nm. Each microfluidic channel hasat least one chemical species that binds to or reacts with the analyte.The one or more detectors measures a change in the resonance frequencyof the one or more beams upon binding or reaction of the analyte.Detection is accomplished by transducing the mass of adsorbed analytemolecules into changes in mechanical resonant frequency.

In one embodiment, the chemical species is a capture ligand that bindsto the analyte. A capture ligand is a molecule that has a high capacityof molecular recognition for another molecule or complex and a highcapacity to specifically bind to the molecule or complex. Unlessspecified as a covalent bond, the term “bind” or “bound” includes bothcovalent and non-covalent associations. “Specific binding,” as usedherein, is when a capture ligand binds one or more other molecule orcomplex (i.e., the target), with specificity sufficient to differentiatebetween the molecule or complex and other components or contaminants ofa sample. In one embodiment, the dissociation constant of the captureligand for the target less than about 1×10⁻⁶ M. In another embodiment,the capture ligand may be one member of a molecular recognition system.Molecular recognition systems for use in the invention are conventionaland are not described here in detail. Techniques for preparing andutilizing such systems are well known in the art and are exemplified inthe publication of Tijssen, P., “Laboratory Techniques in Biochemistryand Molecular Biology Practice and Theories of Enzyme Immunoassays”(1988), eds. Burdon and Knippenberg, New York: Elsevier, the entireteachings of which are incorporated herein. Preferred molecularrecognition systems include an antigen/antibody, an antigen/antibodyfragment, an avidin/biotin, a streptavidin/biotin, a protein A/I_(g) ora lectin/carbohydrate. Either member of the molecular recognition systemmay be a capture ligand. The other member of the molecular recognitionsystem will be the target. In one embodiment, the target of a captureligand is an antigen on the surface of a cell, such as a cell surfacereceptor, an integrin, a transmembrane protein, and ion channel or amembrane transport protein.

Other capture ligands include nucleic acids (e.g., DNA and RNA) ormodified nucleic acids (e.g., DNA or RNA with modified bases or modifiedbackbones). In addition, the nucleic acids may be single stranded ordouble stranded. Nucleic acids and modified nucleic acids generally willbind a target nucleic acid that has a sequence that has at least three,preferably eight, consecutive nucleic acids that are complementary tothe sequence of the capture ligand.

The term “nucleic acids,” or “oligonucleotides,” as used herein, refersto a polymer of nucleotides. Typically, a nucleic acid comprises atleast three nucleotides. The polymer may include natural nucleosides(i.e., adenosine, thymidine, guanosine, cytidine, uridine,deoxyadenosine, deoxythymidine, deoxyguanosine, and deoxycytidine) ormodified nucleosides. Examples of modified nucleotides include basemodified nucleoside (e.g., aracytidine, inosine, isoguanosine,nebularine, pseudouridine, 2,6-diaminopurine, 2-aminopurine,2-thiothymidine, 3-deaza-5-azacytidine, 2′-deoxyuridine, 3-nitorpyrrole,4-methylindole, 4-thiouridine, 4-thiothymidine, 2-aminoadenosine,2-thiothymidine, 2-thiouridine, 5-bromocytidine, 5-iodouridine, inosine,6-azauridine, 6-chloropurine, 7-deazaadenosine, 7-deazaguanosine,8-azaadenosine, 8-azidoadenosine, benzimidazole, M1-methyladenosine,pyrrolo-pyrimidine, 2-amino-6-chloropurine, 3-methyl adenosine,5-propynylcytidine, 5-propynyluridine, 5-bromouridine, 5-fluorouridine,5-methylcytidine, 7-deazaadenosine, 7-deazaguanosine, 8-oxoadenosine,8-oxoguanosine, O(6)-methylguanine, and 2-thiocytidine), chemically orbiologically modified bases (e.g., methylated bases), modified sugars(e.g., 2′-fluororibose, 2′-aminoribose, 2′-azidoribose,2′-O-methylribose, L-enantiomeric nucleosides arabinose, and hexose),modified phosphate groups (e.g., phosphorothioates and5′-N-phosphoramidite linkages), and combinations thereof. Natural andmodified nucleotide monomers for the chemical synthesis of nucleic acidsare readily available (e.g. see, www.trilinkbiotech.com,www.appliedbiosystems.com, www.biogenex.com or www.syngendna.com).

The capture ligand may also be a nucleic acid ligand, such as anaptamers. As used herein, “nucleic acid ligand” is a non-naturallyoccurring nucleic acid that binds selectively to a target. The nucleicacid that forms the nucleic acid ligand may be composed of naturallyoccurring nucleosides, modified nucleosides, naturally occurringnucleosides with hydrocarbon linkers (e.g., an alkylene) or a polyetherlinker (e.g., a PEG linker) inserted between one or more nucleosides,modified nucleosides with hydrocarbon or PEG linkers inserted betweenone or more nucleosides, or a combination of thereof. In one embodiment,nucleotides or modified nucleotides of the nucleic acid ligand can bereplaced with a hydrocarbon linker or a polyether linker provided thatthe binding affinity and selectivity of the nucleic acid ligand is notsubstantially reduced by the substitution (e.g., the dissociationconstant of the nucleic acid ligand for the target should not be greaterthan about 1×10⁻⁶ M). The target molecule of a nucleic acid ligand is athree dimensional chemical structure that binds to the nucleic acidligand. However, when the target is another nucleic acid, the nucleicacid ligand is not simply a linear complementary sequence of a nucleicacid target but may include regions that bind via complementaryWatson-Crick base pairing interrupted by other structures such ashairpin loops). Targets of nucleic acid ligands include small molecules,peptide, polypeptide, carbohydrate and nucleic acid molecules.

Another type of capture ligand is a protein nucleic acid (PNA). A PNAhas a peptide backbone in which a natural or non-natural nucleic acidbase is attached to each amino acid residue. A PNA can recognize anucleic acids that have a complementary sequence of at least threeconsecutive bases, preferably eight consecutive bases, to the sequenceof the PNA.

In one embodiment, the capture ligand is bound to the interior surfaceof the microfluidic channel. One method of binding the capture ligand tothe interior surface of the microfluidic channel is to bind a linker tothe interior surface of the microfluidic channel, then bind the captureligand to the linker. The linker must have one or more groups that willbind to the surface of the microfluidic channel and one or more groupsthat will bind to the capture ligand (such as a primary or secondaryamine, —OH, —SH, or a halo). For example, when the interior surface ofthe microfluidic channel is silicon nitride or silicon dioxide, onemethod of binding the capture ligand to the interior surface of themicrofluidic channel is to contact the surface of the microfluidicchannel with a silane linker. A silane linker is a molecule that has atleast one silyl group that can bind to a silicon dioxide or siliconnitride surface and at least one other group that can bind to thecapture ligand. The capture ligand is then reacted with the freefunctional group, thereby binding the capture ligand to the innersurface of the microfluidic channel. In one embodiment, the captureligand can be represented by the following structural formula:

-   -   wherein:    -   R₁, R₂ and R₃ are each, independently, —H, an alkyl, or an        arylalkyl;    -   L is an alkylene, a cycloalkylene, a heteroalkylene, a        heterocycloalkylene, a sugar residue, or an arylalkylene; and    -   X is an —NHR, —OH, —SH, or a halo, wherein R is —H, an alkyl, an        arylalkyl, or an aryl.

In another embodiment, the interior surface of the microfluidic channelis gold, silver, copper, cadmium, zinc, palladium, platinum, mercury,lead, iron, chromium, manganese, tungsten, or any alloys thereof, andthe linker contains a thiol group which can bind to these surfaces andanother group that can bind to the capture ligand.

When the interior surface of the microfluidic channel is an oxide, suchas silicon dioxide, the linker may have a carboxylic acid group thatwill bind to the oxide surface and another group that can bind to thecapture ligand.

When the interior surface of the microfluidic channel is platinum,palladium or any alloy thereof, the linker may have a nitrile or anisonitrile that can bind to these surfaces and another group that canbind to the capture ligand.

When the interior surface of the microfluidic channel is copper, thelinker may have a hydroxamic acid that can bind to this surface andanother group that can bind to the capture ligand.

An alternative way of binding the capture ligand to the interior surfaceof the microfluidic channels is to select a capture ligand that has agroup that will bind to the interior surface of the microfluidic channelor to modify the capture ligand itself so it contains a group that willbind to the interior surface of the microfluidic channel. For example,the capture ligand may be modified to contain a thiol group that willbind to microfluidic channels that have interior surfaces of gold,silver, copper, cadmium, zinc, palladium, platinum, mercury, lead, iron,chromium, manganese, tungsten, or any alloys thereof.

The sensitivity of the apparatus for detecting a target is improved themore target molecules that are bound in the microfluidic channel. Thus,increasing the number of capture ligand in the microfluidic channel canincrease the sensitivity of the apparatus. One method of increasing thenumber of capture ligands that are in the microfluidic channel is toincrease the surface area by roughening the interior surface of thechannel.

In another embodiment, the number of capture ligands in the microfluidicchannel is increased by putting a porous gel plug in the channel thathas capture ligands bound to the gel. Typically, the gel is prepared bypolymerizing monomer units. The capture ligand may be attached to amonomer unit and added to the prepolymer mixture. When the prepolymermixture is polymerized the capture ligand will be bound directly to thegel. A method of binding nucleic acid capture ligands to a gel isdescribed in U.S. Pat. No. 6,180,770, the entire teachings of which areincorporated by reference. Alternatively, when the capture ligand islarger than the pores of the gel, the capture ligand may be added to theprepolymer mixture. When the prepolymer mixture is polymerized to form agel, the capture ligands are trapped within the pores of the gel. In oneembodiment, the polymerization reaction may be initiated by radiation,such as ultraviolet light. In this embodiment, it is desirable that thewalls of the microfluidic channel are made of a transparent ortranslucent material, such as silicon nitride, so that the prepolymermixture can be injected into the microfluidic channel under pressure andthen polymerized by directing radiation onto a section of the beam wherethe gel is to be polymerized.

One advantageous arrangement for the microfluidic channels is a beam 12that has two microfluidic channels 18 a and 18 b that meet in a regioncontaining a polymerized gel 20 and then separate downstream from thegel (see FIG. 3). In this embodiment, the analyte can be transportedinto the gel via pressure from the fluid flow. Alternatively, when theanalyte is charged, the analyte can be transported into the gel viaelectrophoresis 22.

In one embodiment, the beams of the apparatus of the invention areresonating and the detector measures changes in resonance frequency ofthe beam. Typically, the resonance of each beam is driven by a pair ofelectrodes. In one embodiment, the surface of the beams may be patternedwith a metal that is attached to a power source and serves as one memberof the electrode pair. The other member of the electrode pair issuspended above the surface of the beam. When there is more than onebeam in the apparatus, the metal electrode patterned on the beams may beconnected such that the electrode is common to all beams. The electrodessuspended above each beam, however, are separately addressable.Typically, the electrodes are a metal such as gold, nickel, platinum,aluminum, copper, antimony, tin, indium, chromium, titanium, and alloysthereof. In a preferred embodiment, electrodes are gold.

In one embodiment, the beams are not patterned with a metal electrode.Instead, the solution in the microfluidic channel is an electrolytesolution that is attached to a power source. The electrolytic solutionin the microfluidic channels acts as an electrode and, if eachmicrofluidic channel is connected to the microfluidic channels in otherbeams of the apparatus, the electrolyte solution can act as a commonelectrode for all the beams. In this embodiment, there is a separatelyaddressable electrode suspended above each beam.

In an alternative embodiment, the detector measures changes in surfacestress of the beam. In one embodiment, changes in surface stress may becaused by steric stress caused by analyte molecules packing closely asthey bind to the capture ligands in the microfluidic channel. In thisembodiment, a substantially higher concentration of a capture ligand isbound on one side of the microfluidic channel than on the opposite sideof the microfluidic channel. When the capture ligand binds to ananalyte, the difference in surface stress between the two sides causesthe channel to bend. In this embodiment, the detector measures thedeformation of the beam.

In another embodiment, surface stress may be caused by differentialexpansion of the materials that make up the beam. In this embodiment,one of the outer surfaces of the beam is coated with a thin film whosethermal expansion coefficient is different from that of the channel. Acapture ligand is contained inside the channel. When the capture ligandbinds to an analyte, heat is released or absorbed, and the resultingchange in temperature causes the beam to bend by means of a bimorphaction. In this embodiment, the detector measures the deformation of thebeam.

In another embodiment, the one or more detectors of the apparatus of theinvention are one or more capacitors. Capacitive sensors can measuredisplacement as a change in the capacitance of a plane capacitor. In oneembodiment, the drive electrodes are also used as a capacitivedetectors. Capacitor sensors where the cantilever is one of the twocapacitor plates have been developed by Blanc, et al., J. Vac. Sci.Technolo. B 14: 901 (1996), the entire teachings of which areincorporated herein by reference.

Alternatively, the detector may be an optical lever, in which a laserbeam is reflected from the apex of the beam, or a laser vibrometer,which utilizes a laser to illuminate the beam and measures the frequencyresponse by means of Doppler shifts (see J. Yang, et al., “Mechanicalbehavior of ultrathin microcantilevers,” Sensors and Actuators (2000),82: 102-107, the entire teachings of which are incorporated herein byreference).

Alternatively, the detector may be a piezoresistive or piezoelectric. Inthis embodiment the beam is made of a piezoresistive material whichchanges its electrical conductivity when it is strained.

The signal to noise ratio of the apparatus can be improved by enclosingthe beam of the apparatus in a protected environment such that the beamis protected from changes in humidity, dust accumulation, and otherfactors that may effect the resonance frequency of the beam. Inaddition, since the quality factor is decreased by viscous drag on thebeam from the environment in which the beam is suspended, it isdesirable to have the beam suspended in a low pressure environment toimprove the sensitivity of detection.

In one embodiment of the apparatus of the invention, comprises a devicestructure having at least one suspended beam that contains one or moremicrofluidic channels, wherein each microfluidic channel has at leastone chemical species that binds to or reacts with the analyte; a samplefluid channel connected to the inlet of at least one of the microfluidchannel, wherein the sample fluid channel has a depth that issubstantially larger than the microfluidic channel; and one or moredetectors for measuring a change in the one or more suspended beams uponbinding or reaction of the analyte. This embodiment of the apparatus ofthe invention is a micro-electro-mechanical system (MEMS). In apreferred embodiment, the MEMS of the invention has a packagingstructure that covers the device region and provides connections betweenthe sample fluid channels and the microfluidic channels of the device.In addition the packaging structure can be constructed to provide a lowpressure environment in which the beam is suspended.

Typically, each of the microfluidic channels has a depth in the range ofbetween about 100 nm and about 1000 nm, and each of the sample fluidchannels has a depth in the range of between about 10 μm and 100 μm.

The detector of the apparatus may measure changes in the frequency ofthe beam upon binding or reaction of an analyte or it may measuredeformation of the beam upon binding or reaction of the analyte. Whenthe apparatus has a resonating beam, the resonance of each beam isdriven by a pair of drive electrodes as discussed above. In oneembodiment, one of the electrodes of the electrode pair is common to allthe beams and the other electrode of the electrode pair is suspendedabove the beam and is separately addressable for each beam. Preferably,the packaging structure includes the separately addressable electrodes.

In one embodiment, the substrate is bound to the MEMS via apolydimethylsiloxane gasket. In this embodiment, the substrate can bemade of glass, a ceramic, a plastics, a circuit board, and a siliconchip (with or without additional circuitry). For example (see FIG. 4),the connection between the microfluidic channels and the sample fluidchannels are patterned in a polydimethylsiloxane gasket 25 (see Duffy,Anal. Chem. (1998), 70: 4974, the entire teachings of which areincorporated herein by reference). The gasket is then bonded to asubstrate 24 that has been patterned with the separately addressableelectrodes 26 that will be suspended above each beam once the packagingstructure is bound to the device. It is desirable to heat the substrateand the gasket after plasma-bonding as it generally improves adhesionbetween the gasket and the substrate. The surface of the device can becoated with a metal which forms the common electrode 28 or can be leftuncoated when an electrolyte solution in the microfluidic channels formsthe common electrode. Then the gasket is clamped to the device 30 and/orplasma-bonded to the device. Holes 32 may be etched or drilled in thesubstrate through which the sample fluids may be added to the device.The common electrode and the separately addressable electrodes may beused as capacitive detectors. Alternatively, the apparatus may have anoptical lever detector in which a laser beam is aligned with aresonating section of the beam such that it reflects off the beam. Theposition of the reflected laser beam is then detected by a detector andthe position of the reflected beam is transduced into information aboutthe resonance frequency of the beam. When the apparatus has more thanone beam, one laser is aligned with each beam.

In another embodiment (see FIG. 5), the packaging structure is a glassor a silicon chip 34 substrate that has cavities 38 for the each beamand the connections between the sample fluid channels 36 and themicrofluidic channels etched into the substrate. The separatelyaddressable electrodes 26 are recessed in the cavity of the substratethat will be aligned above each beam. The surface of the device can becoated with a metal which forms the common electrode 28 or can be leftuncoated when an electrolyte solution in the microfluidic channels formsthe common electrode. Finally, the substrate is joined to the device 30by anodic bonding such that the separately addressable electrodes arealigned above the beam and the sample fluid channels connect with themicrofluidic channels. Holes 32 for introduction of the sample fluid maybe drilled or etched into the substrate or may be etched through thedevice. The common electrode and the separately addressable electrodesmay be used as capacitive detectors. Alternatively, the apparatus mayhave an optical lever detector in which a laser beam is aligned with aresonating section of the beam such that it reflects off the beam. Theposition of the reflected laser beam is then detected by a detector andthe position of the reflected beam is transduced into information aboutthe resonance frequency of the beam. When the apparatus has more thanone beam, one laser is aligned with each beam.

In another embodiment, the substrate is patterned with the separatelyaddressable electrodes 26 (FIG. 6A) and a photoresist layer 40 is addedto the surface of the substrate that has the patterned electrodes (FIG.6B). The photoresist layer is irradiated through a mask, then removedfrom areas that will form the walls of the connection between the samplefluid and the microfluidic channel 42 a and 42 b and areas that willdefine the walls of the cavity 44 in which the beam will be suspended. Ametal, such as gold, nickel, platinum, aluminum, copper, antimony, tin,indium, chromium, titanium, and alloys thereof, is then added to theopen areas in the photoresist (FIG. 6C). Then the photoresist is removedleaving the metal walls that form the walls of the connection betweenthe sample fluid and the microfluidic channel and areas that will definethe walls of a cavity in which the beam will be suspended (FIG. 6D). Thesurface of the device can be coated with a metal which forms the commonelectrode 28 or can be left uncoated when an electrolyte solution in themicrofluidic channels forms the common electrode. Finally, the substrateis joined to the device 30 by, for example, soldering the metal walls tothe common electrode on the surface of the device, such that theseparately addressable electrodes are aligned above the beam and thesample fluid channels connect with the microfluidic channels (FIG. 6E).Holes for introduction of the sample fluid may be drilled or etched intothe substrate or may be etched through the device (not shown). Thecommon electrode and the separately addressable electrodes may be usedas capacitive detectors. Alternatively, the apparatus may have anoptical lever detector in which a laser beam is aligned with aresonating section of the beam such that it reflects off the beam. Theposition of the reflected laser beam is then detected by a detector andthe position of the reflected beam is transduced into information aboutthe resonance frequency of the beam. When the apparatus has more thanone beam, one laser is aligned with each beam.

Until now microfluidic channel detectors have not yet been integratedwith conventional microfluidics. Decreasing the channel thickness andthe thickness of the walls of the channel, as well as, increasing thenumber of capture ligands bound to the interior of the channel shouldincrease the resolution. While integrating microfluidic channeldetectors with conventional microfluidics will increase the utility ofsuch detectors and allow multiple detectors to be fabricated on onesemiconductor wafer (FIG. 7).

The microfluidic channels of the invention can be fabricated bydepositing a first layer 48 of a material that will make up one side ofthe microfluidic channel wall on a semiconductor wafer 46 having one ormore trenches (FIGS. 8A, 8B and 8C. In one embodiment, the semiconductorwafer is a silicon wafer and the channel wall material is siliconnitride or silicon dioxide. A sacrificial layer 50, such as apolysilicon layer, is then deposited on the first insulator layer (FIG.8D). Then the sacrificial layer is removed via a planarizationtechnique, such as chemical-mechanical planarization, down to the firstchannel layer 48, thereby exposing a planar surface of the first channellayer having the sacrificial layer in the trenches (FIG. 8E). A secondchannel layer 52, such as a silicon nitride layer or a silicon dioxidelayer, is deposited on the planar surface forming the other side of themicrofluidic channel (FIG. 8F). Then one or more holes 54 are etched inthe second channel layer that connected to one or more of the trenches(FIG. 8G). The sacrificial layer is removed from the trenches byetching, thereby forming a microfluidic channel (FIG. 8H). When thesacrificial layer is polysilicon, it can be etched by treating it with asolution of potassium hydroxide. A portion of the backside of thesemiconductor wafer is removed below the microfluidic channel, forexample via etching, thereby forming a suspended beam containing themicrofluidic channel (FIG. 8H). This step may be done simultaneouslywith etching away the sacrificial layer to form the microfluidicchannel. The interior of the microfluidic channels can then befunctionalized as described above either before or after the device isbound to a packaging structure.

In one embodiment, it is desirable that the microfluidic channel isconductive. One method of forming a conductive microfluidic channel isto dope a portion of the polysilicon sacrificial layer with a p-typeand/or an n-type dopant. Since heavily doped polysilicon (e.g.,polysilicon having a dopant concentration of 5×10¹⁹ cm⁻³) is resistantto etching with potassium hydroxide, when the sacrificial layer isremoved by etching with a potassium hydroxide solution, the dopedportion of the polysilicon layer will remain in the microfluidicchannel. Another method of forming a conductive microfluidic channel isto form the first and/or the second channel walls from dopedpolysilicon.

The method of the invention allows microfluidic channels to be formedthat have a depth in the range of between about 50 nm and about 2000 nm.In one embodiment the depth of the microfluidic channels in the range ofbetween about 100 nm and about 1000 nm. In addition, microfluidicchannels can be fabricated that have very thin wall with the method ofthe invention. For example, microfluidic channels can be fabricated thathave a wall thickness in the range of between about 100 nm and about1200 nm. Thus, the method of the invention is advantageous sincesuspended beam detectors are more sensitive the thinner the microfluidicchannels and the walls of the microfluidic channels.

These and other aspects of the present invention will be furtherappreciated upon consideration of the following Examples, which areintended to illustrate certain particular embodiments of the inventionbut are not intended to limit its scope, as defined by the claims.

EXAMPLES

As described above, suspended microchannels for molecular detection mustbe sufficiently thin, and additionally they must be configured forcontinuous fluidic delivery for real-time measurements. To address bothof these requirements, we combined a polysilicon Damascene process,sacrificial layer etching in hot potassium hydroxide, and bulkmicromachining to fabricate suspended microchannels with a wallthickness of 800 nm and a fluid layer thickness of 1.2 μm. First, weetched microfluidic trenches in a standard <100>silicon wafer usingphotolithography and reactive ion etching (RIE). The wafer wassubsequently coated with 800 nm low-stress low-pressure chemical vapordeposited silicon nitride and followed by a 1.5 μm layer of polysilicon.The polysilicon layer was planarized with chemical mechanical polishing(CMP). The CMP process was timed to stop as soon as it reaches thesilicon nitride layer so that the trenches remain filled withpolysilicon. After the CMP, a second layer of low-stress silicon nitridewith the same thickness as the first layer was deposited. This layerclosed the microfluidic channels, which were filled with polysilicon.Again, standard photolithography and RIE was used to make an opening inthe silicon nitride layer which provided access ports to the polysiliconfilled microfluidic channel and to remove a portion of the backside ofthe wafer up to the silicon nitride layer in order to form the suspendedchannel. The wafer backside was also patterned in the same step todefine the locations of through-holes under the suspended sections ofthe channel. Finally, the sacrificial polysilicon and the waferthrough-holes was etched in a 6M aqueous potassium hydroxide solution at80° C. We found that at this temperature, diffusion did not severelylimit the etch rate for the sacrificial layer. We were able tocompletely release channels up to 1 mm in less than 20 h with a yield of80%. (See FIG. 8 for a flow diagram of this method).

An electron micrograph of three suspended microchannels is shown in FIG.9 a, and a phase contrast optical image is shown in FIG. 9 b. To obtaincontinuous fluidic delivery to the suspended channels, a microfluidicnetwork made of poly(dimethylsiloxane) (PDMS) was bonded to the chipsurface. The inlets to the nitride channels were located within U-shapedchannels in the PDMS so that solutions could be transported with lowflow resistance to the low-volume microchannels. The device was actuatedelectrostatically, and the deflection was measured with the opticallever method. Good electrical conductivity and high optical reflectivitywere achieved by coating the suspended channels with a 100 nm aluminumthin film. The aluminum was connected to ground, and a drive electrodewas brought to within 50 μm of the device by means of a micrometerstage.

Frequency responses were recorded using a function generator infrequency sweep mode and a lock-in amplifier. To obtain time-plots ofthe resonance frequency, the device was placed in a feedback loop, withthe output of the deflection sensor connected directly to the driveelectrode via a saturating voltage amplifier with ±5V output swing. Thedrive signal was offset by +60V with respect to ground, and theoscillation frequency was measured by means of a frequency counter. Inthis configuration we observed a frequency noise level of 80 mHz rms ina 4 mHz to 4 Hz measurement bandwidth.

In order to evaluate the mass resolution, we measured the frequencyresponse for a 300 μm cantilever in the unfilled state, as well asfilled with isopropyl alcohol, and filled with water. The resultingspectra are shown in FIG. 10. Note that the quality factor in eachremains the same which indicating that energy loss of a fluid-filledmicrochannel is not increased by the viscous drag associated with thesolution enclosed in the microfluidic channels. This is because thesmall volume of the microchannel (˜27 pL) and the small vibrationamplitude (<<1 μm) results in very few water molecules being transferredduring each oscillation cycle.

Taking into account the known mass densities of the different media andthe design volume of 27 pL, we find a mass sensitivity of 107 mHz/pg forsmall loadings of a water filled microchannel. Given this sensitivitytogether with the 80 mHz noise level and a surface area of 53000 μm 2,our current detection limit is approximately 1.4×10⁻¹⁷ g/μm² over a 4mHz to 4 Hz bandwidth.

We demonstrated biomolecular detection by functionalizing the interiorchannel walls with biotinylated Bovine Serum Albumin (bBSA) andperforming several experiments to detect the subsequent binding ofavidin and bBSA. Constant fluid pressure was maintained at all times,except during the switching between reagents. Avidin and bBSA weredissolved in phosphate buffered saline (PBS) at 500 μg/mL and 1 mg/mL,respectively. The results of these experiments are summarized in FIG.11. Each section represents the relative frequency shift over time,zeroed at the point at which fluids were switched. FIG. 1A shows thebaseline signal after disconnecting and reconnecting buffer. FIG. 11B isthe result of switching from buffer to avidin solution. The resonancefrequency dropped sharply by more than 2 Hz a few seconds after changingfluids. This delay was expected due to the time required for the liquidto flow from the point of switching to the beginning of the suspendedchannel. When we switched back to buffer, the resonance frequencyremained unchanged, indicating that fluid density difference did notcause the signal. Next, we verified that the frequency also remainedunchanged when we re-injected avidin into the buffer filledmicrochannel. This suggests that all available binding sites for avidinhad already been occupied. Next, we switched to bBSA solution, followedagain by avidin. In both cases, a rapid drop in resonance frequencycould be observed (FIGS. 11C and 11D). The fact that the injection ofbBSA restored the ability to detect avidin in the resonatingmicrochannel can be explained by bBSA-avidin multilayer formation, asillustrated schematically in FIG. 11. Since there are several biotinsattached to each BSA molecule, a new bBSA layer can provide many bindingsites for the subsequent adsorption of avidin.

None of the binding and control experiments described previouslyrevealed frequency shifts from changes in volumetric density betweenbuffer and bBSA or avidin. Although we estimate that these solutionsshould shift the frequency by a few hundred millihertz, we found thatthe complete exchange of fluid within the suspended microchannel oftenrequired several minutes. Over this time-scale, frequency shifts below˜1 Hz would have been obscured by drift, which was often present. Incontrast, the high binding affinity of biotin-avidin results in rapidsaturation of the surface concentration even at a fraction of the volumeconcentration that we injected.

Our results demonstrate that the relatively large surface area to volumeratio of the microchannel is advantageous for mass detection. Once adilute sample enters the microchannel, the molecules are quicklydepleted as they bind to the immobilized capture ligand. As additionalmolecules enter, the surface soon collects many more molecules than arepresent in the surrounding solution. As a result, the enhanced channelconcentration produces a measurable change in resonance frequency.

1. An apparatus for detecting an analyte or measuring a property of ananalyte, comprising: a) at least one suspended beam connected to twomechanically stable supports, wherein the beam contains one or moremicrofluidic channels, and wherein each microfluidic channel has atleast one chemical species that binds to or reacts with the analyte; andb) one or more detectors for measuring a change in the one or more beamsupon binding or reaction of the analyte.
 2. The apparatus of claim 1,wherein the chemical species is a capture ligand that binds to theanalyte.
 3. The apparatus of claim 2, wherein the one or more beams areresonating and the detector measures changes in resonance frequency ofthe beam.
 4. The apparatus of claim 3, wherein the capture ligand isbound to the interior surface of the microfluidic channel.
 5. Theapparatus of claim 3, further comprising a gel in the microfluidicchannel, wherein the capture ligand is bound to the gel.
 6. Theapparatus of claim 5, wherein the beam has two microfluidic channelsthat meet in a region containing a polymerized gel then separatedownstream from the gel.
 7. The apparatus of claim 6, wherein theanalyte is transported into the gel via pressure from the fluid flow. 8.The apparatus of claim 6, wherein the analyte is transported into thegel via electrophoresis.
 9. The apparatus of claim 3, wherein theresonance of each beam is driven by a pair of electrodes.
 10. Theapparatus of claim 9, wherein one of the electrodes of the electrodepair is common to all the beams and the other electrode of the electrodepair is separately addressable for each beam.
 11. The apparatus of claim10, wherein the electrodes are a metal that is, independently, selectedfrom the group consisting of gold, nickel, platinum, aluminum, copper,antimony, tin, indium, chromium, titanium, and alloys thereof.
 12. Theapparatus of claim 11, wherein the electrodes are gold.
 13. Theapparatus of claim 10, wherein the common electrode is in contact withthe each beam.
 14. The apparatus of claim 10, wherein the solution inthe microfluidic channel is an electrolyte solution and the electrolytesolution is the common electrode.
 15. The apparatus of claim 3, whereinthe one or more detectors are one or more capacitors.
 16. The apparatusof claim 15, wherein the drive electrodes are also used as a capacitivedetectors.
 17. The apparatus of claim 16, wherein one of the twocapacitor plates of each capacitive detector is in contact with thesurface of the beam.
 18. The apparatus of claim 3, wherein the detectoris an optical lever or a laser vibrometer.
 19. The apparatus of claim 3,wherein the capture ligand is a nucleic acid.
 20. The apparatus of claim19, wherein the capture ligand is a single stranded DNA.
 21. Theapparatus of claim 19, wherein the capture ligand is double strandedDNA.
 22. The apparatus of claim 3, wherein the capture ligand is aprotein, peptide or a protein nucleic acid (PNA).
 23. The apparatus ofclaim 22, wherein the capture ligand is an antibody or an antibodyfragment.
 24. The apparatus of claim 3, wherein the capture ligand is anantigen.
 25. The apparatus of claim 22, wherein the capture ligand is alectin.
 26. The apparatus of claim 3, wherein the capture ligand is acarbohydrate.
 27. The apparatus of claim 26, wherein the capture ligandis a sugar residue.
 28. The apparatus of claim 2, wherein the detectormeasures the conductivity of the microfluidic channel.
 29. The apparatusof claim 2, wherein the detector measures deformation of the beam. 30.The apparatus of claim 29, wherein capture ligand is bound to theinterior surface of the microfluidic channel, and wherein there is asubstantially higher concentration of capture ligand on one side of themicrofluidic channel than on the opposite side.
 31. The apparatus ofclaim 29, wherein the one or more detectors are one or more capacitors.32. The apparatus of claim 31, wherein one of the two capacitor platesof each capacitive detector is in contact with the surface of the beam.33. The apparatus of claim 29, wherein the detector is an optical lever.34. The apparatus of claim 29, wherein the capture ligand is a nucleicacid.
 35. The apparatus of claim 34, wherein the capture ligand is asingle stranded DNA.
 36. The apparatus of claim 34, wherein the captureligand is double stranded DNA.
 37. The apparatus of claim 29, whereinthe capture ligand is a protein, peptide or a protein nucleic acid(PNA).
 38. The apparatus of claim 37, wherein the capture ligand is anantibody or an antibody fragment.
 39. The apparatus of claim 29, whereinthe capture ligand is an antigen.
 40. The apparatus of claim 29, whereinthe capture ligand is a lectin.
 41. The apparatus of claim 40, whereinthe capture ligand is a carbohydrate.
 42. The apparatus of claim 41,wherein the capture ligand is a sugar residue.
 43. The apparatus ofclaim 1, wherein the depth of the one or more microfluidic channels isin the range of between about 100 nm and about 3000 nm.
 44. Theapparatus of claim 43, wherein the walls of the microfluidic channelhave a thickness in the range of between about 100 nm and 1200 nm. 45.The apparatus of claim 44, wherein an inlet to the microfluidic channelis connected to a sample fluid channel having a depth in the range ofbetween about 10 μm and about 100 μm.
 46. The apparatus of claim 1,wherein the beam is suspended in a low pressure environment.
 47. Anapparatus for detecting an analyte or measuring a property of ananalyte, comprising: a) a device structure having at least one suspendedbeam that contains one or more microfluidic channels, wherein eachmicrofluidic channel has at least one chemical species that binds to orreacts with the analyte; and b) a sample fluid channel connected to theinlet of at least one of the microfluid channel, wherein the samplefluid channel has a depth that is substantially larger than themicrofluidic channel.
 48. The apparatus of claim 47, wherein theapparatus is a micro-electro-mechanical system (MEMS) having a packagingstructure that covers the device region.
 49. The apparatus of claim 48,wherein each of the microfluidic channels has a depth in the range ofbetween about 100 nm and about 3000 nm, and each of the sample fluidchannels has a depth in the range of between about 10 μm and 100 μm. 50.The apparatus of claim 49, wherein the walls of the microfluidic channelhave a thickness in the range of between about 100 nm and 1200 nm. 51.The apparatus of claim 49, wherein the sample fluid channels arepatterned in the packaging structure.
 52. The apparatus of claim 51,wherein the chemical species is a capture ligand that binds to theanalyte.
 53. The apparatus of claim 52, further including one or moredetectors.
 54. The apparatus of claim 53, wherein the one or more beamsare resonating and the detector measures changes in resonance frequencyof the beam.
 55. The apparatus of claim 54, wherein the suspended beamis a cantilever.
 56. The apparatus of claim 54, wherein the suspendedbeam is connected to two mechanically stable supports.
 57. The apparatusof claim 54, wherein the capture ligand is bound to the interior surfaceof the microfluidic channel.
 58. The apparatus of claim 54, furthercomprising a gel in the microfluidic channel, wherein the capture ligandis bound to the gel.
 59. The apparatus of claim 56, wherein the beam hastwo microfluidic channels that meet in a region containing a polymerizedgel then separate downstream from the gel, wherein the gel comprises acapture ligand.
 60. The apparatus of claim 59, wherein the analyte istransported into the gel via pressure from the fluid flow.
 61. Theapparatus of claim 59, wherein the analyte is transported into the gelvia electrophoresis.
 62. The apparatus of claim 54, wherein theresonance of each beam is driven by a pair of electrodes.
 63. Theapparatus of claim 62, wherein one of the electrodes of the electrodepair is common to all the beams and the other electrode of the electrodepair is separately addressable for each beam.
 64. The apparatus of claim63, wherein the electrodes are a metal, independently, selected from thegroup consisting of gold, nickel, platinum, aluminum, copper, antimony,tin, indium, chromium, titanium, and alloys thereof.
 65. The apparatusof claim 64, wherein the electrodes are gold.
 66. The apparatus of claim63, wherein the packaging structure comprises the separately addressableelectrodes.
 67. The apparatus of claim 66, wherein the common electrodeis in contact with the each beam.
 68. The apparatus of claim 66, whereinthe solution in the microfluidic channel is an electrolyte solution andthe electrolyte solution is the common electrode.
 69. The apparatus ofclaim 54, wherein the one or more detectors are one or more capacitors.70. The apparatus of claim 69, wherein the drive electrodes are alsoused as a capacitive detector.
 71. The apparatus of claim 70, whereinone of the two capacitor plates is in contact with the surface of thebeam.
 72. The apparatus of claim 71, wherein the packaging structurecomprises a substrate made of a material selected from the groupconsisting of glass, a ceramic, a plastics, a circuit board, and asilicon chip.
 73. The apparatus of claim 54, wherein the one or moredetectors are optical lever detectors or laser vibrometers.
 74. Theapparatus of claim 72 or 73, wherein the substrate is bound to the MEMSvia a polydimethylsiloxane gasket.
 75. The apparatus of claim 74,wherein the connection between the microfluidic channels and the samplefluid channels are patterned in the polydimethylsiloxane gasket.
 76. Theapparatus of claim 77, wherein the common electrode is a patternedmetallic layer on the surface of the MEMS that is bound to the gasket.77. The apparatus of claim 72 or 73, wherein the substrate is glass or asilicon chip and is bound to the MEMS via anodic bonding.
 78. Theapparatus of claim 77, wherein the connection between the microfluidicchannels and the sample fluid channels are patterned in the substrate.79. The apparatus of claim 78, wherein the common electrode is apatterned metallic layer on the surface of the MEMS that is bound to thesubstrate.
 80. The apparatus of claim 72 or 73, wherein substrate isbound to the MEMS via a patterned metallic layer.
 81. The apparatus ofclaim 80, wherein the connection between the microfluidic channels andthe sample fluid channels are patterned in the metallic layer.
 82. Theapparatus of claim 53, wherein the capture ligand is a nucleic acid. 83.The apparatus of claim 82, wherein the capture ligand is a singlestranded DNA.
 84. The apparatus of claim 82, wherein the capture ligandis double stranded DNA.
 85. The apparatus of claim 53, wherein thecapture ligand is a protein, peptide or a protein nucleic acid (PNA).86. The apparatus of claim 85, wherein the capture ligand is an antibodyor an antibody fragment.
 87. The apparatus of claim 53, wherein thecapture ligand is an antigen.
 88. The apparatus of claim 53, wherein thecapture ligand is a lectin.
 89. The apparatus of claim 53, wherein thecapture ligand is a carbohydrate.
 90. The apparatus of claim 89, whereinthe capture ligand is a sugar residue.
 91. The apparatus of claim 53,wherein the detector measures deformation of the beam.
 92. The apparatusof claim 53, wherein capture ligand is bound to the interior surface ofthe microfluidic channel.
 93. The apparatus of claim 92, wherein thereis a substantially higher concentration of capture ligand on one side ofthe microfluidic channel than on the opposite side.
 94. The apparatus ofclaim 92, wherein a surface of the beam is coated with a material havinga different coefficient of thermal expansion from that of the beam. 95.The apparatus of claim 93 or 94, wherein the one or more detectors areone or more capacitors.
 96. The apparatus of claim 95, wherein thepackaging structure comprises one of the capacitor plates of eachcapacitor and the other capacitor plate is in contact with the surfaceof the suspended beam.
 97. The apparatus of claim 9, wherein the one ormore detectors are optical lever detectors.
 98. The apparatus of claim92, wherein the capture ligand is a nucleic acid.
 99. The apparatus ofclaim 98, wherein the capture ligand is a single stranded DNA.
 100. Theapparatus of claim 98, wherein the capture ligand is double strandedDNA.
 101. The apparatus of claim 92, wherein the capture ligand is aprotein or peptide.
 102. The apparatus of claim 101, wherein the captureligand is an antibody or an antibody fragment.
 103. The apparatus ofclaim 92, wherein the capture ligand is an antigen.
 104. The apparatusof claim 92, wherein the capture ligand is a lectin.
 105. The apparatusof claim 92, wherein the capture ligand is a carbohydrate.
 106. Theapparatus of claim 105, wherein the capture ligand is a sugar residue.107. A semiconductor wafer comprising more than one apparatus of claim48.
 108. A method of fabricating a functionalized microfluidic channelhaving an inlet and an outlet, comprising the steps of: a) depositing afirst channel layer on a semiconductor wafer having one or moretrenches; b) depositing a sacrificial layer on the first channel layer;c) removing the sacrificial layer via planarization down to the firstchannel layer, thereby exposing a planar surface of the first channellayer having the sacrificial layer in the trenches; d) depositing asecond channel layer on the planar surface; e) forming one or more holesin the second channel layer connected to one or more of the trenches; f)removing the sacrificial layer, or a portion thereof, from the trenchesby etching, thereby forming a microfluidic channel; and g)functionalizing the interior of the microfluidic channel with a captureligand.
 109. The method of claim 108, wherein a portion of thesemiconductor wafer is removed below the microfluidic channel, therebyforming a suspended beam containing the microfluidic channel.
 110. Themethod of claim 109, wherein the portion of the semiconductor wafer isremoved by etching the wafer from the backside below the microfluidicchannel until the first channel layer is reached.
 111. The method ofclaim 110, wherein the portion of the backside of the semiconductorwafer is removed simultaneously with removal of the sacrificial layerfrom the trenches.
 112. The method of claim 108, wherein: a) thesemiconductor wafer is a silicon wafer; b) the first and the secondchannel layers are silicon nitride or silicon dioxide; and c) thesacrificial layer is polysilicon.
 113. The method of claim 112, furthercomprising the step of doping a section of the sacrificial layer,wherein the doped section of the sacrificial layer remains in thechannel after etching.
 114. The method of claim 108, wherein the firstand the second channel layers are doped polysilicon.
 115. The method ofclaim 108, wherein the microfluidic channel has a depth in the range ofbetween about 100 nm and about 3000 nm.
 116. The method of claim 115,wherein the first and the second channel layers have a thickness in therange of between about 100 nm and about 1200 nm.
 117. The method ofclaim 108, wherein the step of functionalizing the interior of themicrofluidic channel comprises binding a capture ligand to an innersurface of the microfluidic channel.
 118. The method of claim 112 or114, wherein the step of functionalizing the interior of themicrofluidic channel with a capture ligand, comprises the steps of: a)contacting the surface of the microfluidic channel with a silane linker,thereby binding the silane linker to the inner surface of themicrofluidic channel; and b) reacting the capture ligand with the silanelinker, thereby binding the capture ligand to the inner surface of themicrofluidic channel.
 119. The method of claim 118, wherein the silanelinker can be represented by the following structural formula:

wherein: R₁, R₂ and R₃ are each, independently, —H, an alkyl, or anarylalkyl; L is an alkylene, a cycloalkylene, a heteroalkylene, aheterocycloalkylene, a sugar residue, or an arylalkylene; and X is an—NHR, —OH, —SH, a halo, wherein R is —H, an alkyl, an arylalkyl, or anaryl.
 120. The method of claim 118, wherein the capture ligand isselected from the group consisting of a nucleic acid, a single strandedDNA, a double stranded DNA, a protein nucleic acid (PNA), a protein,peptide, an antibody, an antibody fragment, an antigen, a lectin, acarbohydrate, and a sugar residue.
 121. The method of claim 108, whereinthe step of functionalizing the interior of the microfluidic channelcomprises polymerizing a gel in the interior of the microfluidicchannel, wherein the gel comprises one or more capture ligand.
 122. Themethod of claim 121, wherein polymerization of the gel is initiated byradiation.
 123. The method of claim 121, wherein the capture ligand isselected from the group consisting of a nucleic acid, a single strandedDNA, a double stranded DNA, a protein nucleic acid (PNA), a protein,peptide, an antibody, an antibody fragment, an antigen, a lectin, acarbohydrate, and a sugar residue.
 124. The method of claim 108, whereinthe polysilicon is removed from the trenches by etching with an aqueoussolution of KOH.
 125. The method of claim 108, wherein the polysiliconlayer is planarized via chemical-mechanical polishing
 126. The method ofclaim 108, wherein the first and the second silicon nitride layers arelow-stress layers and are deposited using low-pressure chemical vapordeposition.
 127. The method of claim 126, wherein the first and thesecond silicon nitride layers have a thickness in the range of betweenabout 100 nm and about 1200 nm.
 128. A method of packaging a devicecomprising one or more suspended microfluidic channel formed in asemiconductor wafer, comprising the steps of: a) patterning a substratewith one or more separately addressable electrodes, wherein theelectrodes can be aligned with each microfluidic channel of the device;b) preparing a poly(dimethyl siloxane) gasket having one or more fluidchannels and one or more opening; c) bonding the gasket to thesubstrate; d) patterning a common electrode on the surface of thedevice, wherein the common electrode is formed on each microfluidicchannel; e) bonding the gasket to the device, wherein the fluid channelsof the gasket connect with the inlets and outlets of the microfluidicchannels of the device and each opening on the gasket is aligned withone or more suspended microfluidic channel.
 129. The method of claim128, further comprising the step of forming one or more holes in thesubstrate connected to the fluid channels of the gasket.
 130. The methodof claim 128, wherein the gasket is bonded to the substrate via plasmabonding.
 131. The method of claim 130, wherein the gasket is bonded tothe device via plasma bonding.
 132. The method of claim 128, wherein thegasket has a thickness in the range of between about 10 μm and about 100μm.
 133. The method of claim 128, wherein the microfluidic channels ofthe device have a depth in the range of between about 100 nm and about3000 nm.
 134. The method of claim 133, wherein the walls of themicrofluidic channel have a thickness in the range of between about 100nm and about 1200 nm.
 135. The method of claim 134, wherein the fluidchannels of the gasket have a depth of between about 10 μm and about 100μm.
 136. The method of claim 128, wherein the common electrode and theseparately addressable electrodes are made of a material that is,independently, selected from the group consisting of gold, nickel,platinum, aluminum, copper, antimony, tin, indium, chromium, titanium,and alloys thereof.
 137. The method of claim 136, wherein both thecommon electrode and the separately addressable electrodes are made ofgold.
 138. The method of claim 128, wherein the substrate is made of amaterial selected from the group consisting of a ceramic, glass, aplastic, a circuit board, and a silicon chip.
 139. The method of claim138, wherein the substrate is glass.
 140. A method of packaging a devicecomprising one or more suspended microfluidic channel formed in asemiconductor wafer, comprising the steps of: a) forming one or morefluid channel and one or more cavities in a substrate, wherein thecavities can be aligned with the microfluidic channels; b) patterningthe cavities of the substrate with one or more separately addressableelectrodes, thereby forming electrodes that can be aligned with eachmicrofluidic channel of the device; c) patterning a common electrode onthe surface of the device, wherein the common electrode is formed oneach microfluidic channel; d) bonding the substrate to the device,wherein the fluid channels of the substrate connect with the inlets andoutlets of the microfluidic channels of the device and each trench ofthe substrate is aligned with one or more suspended microfluidicchannel.
 141. The method of claim 140, further comprising the step offorming one or more holes in the substrate that connect to the fluidchannels of the substrate.
 142. The method of claim 140, furthercomprising the step of etching one or more openings in the semiconductorwafer that connect to the fluid channels of the substrate.
 143. Themethod of claim 140, wherein the substrate is made from a materialselected from the group consisting of a ceramic, glass, a plastic, and asilicon chip.
 144. The method of claim 143, wherein the substrate isglass or a silicon chip and the fluid channels and one or more cavitiesare etched in the substrate.
 145. The method of claim 144, wherein thesubstrate is glass or a silicon chip and is anodically bonded to thedevice.
 146. The method of claim 140, wherein the microfluidic channelsof the device have a depth of between about 100 nm and about 3000 nm.147. The method of claim 146, wherein the walls of the microfluidicchannel have a thickness in the range of between about 100 nm and about1200 nm.
 148. The method of claim 147, wherein the fluid channels of thesubstrate have a depth of between about 10 μm and about 100 μm.
 149. Themethod of claim 140, wherein the common electrode and the separatelyaddressable electrodes are made of a material that is, independently,selected from the group consisting of gold, nickel, platinum, aluminum,copper, antimony, tin, indium, chromium, titanium, and alloys thereof.150. The method of claim 149, wherein both the common electrode and theseparately addressable electrodes are made of gold.
 151. A method ofpackaging a device comprising one or more suspended microfluidic channelformed in a semiconductor wafer, comprising the steps of: a) patterninga surface of a substrate with one or more separately addressableelectrodes; b) forming a photoresist on the surface of the patternedsubstrate; c) irradiating the photoresist through a mask, therebyremoving the photoresist from predetermined areas of the substrate; d)electroplating a metal in the area of the substrate where thephotoresist was removed, thereby forming the walls of the one or moremicrofluidic channels and the walls of the one or more cavities; e)removing the remainder of the photoresist; f) patterning a commonelectrode on a surface of the device having an inlet and an out let foreach of the microfluidic channels; g) bonding the electroplated metal tothe common electrode, wherein the fluid channels formed by theelectroplated metal walls connect with the inlets and outlets of themicrofluidic channels of the device and each cavity formed by theelectroplated metal walls is aligned with one or more suspendedmicrofluidic channel.
 152. The method of claim 151, further comprisingthe step of forming one or more holes in the substrate that connect tothe fluid channels.
 153. The method of claim 151, further comprising thestep of etching one or more openings in the semiconductor wafer thatconnect to the fluid channels.
 154. The method of claim 151, wherein thesubstrate is made from a material selected from the group consisting ofa ceramic, glass, a plastic, and a silicon chip.
 155. The method ofclaim 154, wherein the substrate is glass.
 156. The method of claim 151,wherein the electroplated metal is soldered to the common electrode.157. The method of claim 156, wherein the soldering material used istin, lead, gold, or alloys thereof.
 158. The method of claim 151,wherein the microfluidic channels of the device have a depth of betweenabout 100 nm and about 3000 nm.
 159. The method of claim 158, whereinthe walls of the microfluidic channel have a thickness in the range ofbetween about 100 nm and about 1200 nm.
 160. The method of claim 151,wherein the fluid channels have a depth of between about 10 μm and about100 μm.